A three-dimensional (3D) two-phase hydrodynamic-pollutant-coupled mathematical model for an open channel confluence of rectangular cross section with equal width was established. The pollutant was considered conservative and the degradation effect was not taken into account.Based on the Reynolds stress model, the geometric characteristics of separation zone and the pollutant transport laws under different junction angles were quantitatively analyzed. The calculation results show that the geometry of the separation zone and pollutant distribution at the confluence have obvious 3D characteristics and are affected by the junction angles. The geometric symmetry of the separation zone is stronger when junction angle is larger. The pollutant distribution is different because of different locations of the secondary flow under different junction angles. The maximum width of the pollution zone and the width of the mixing interface increase with the junction angle.The mixing rate of pollutants upstream of the separation zone increases with junction angles.Downstream of the velocity recovery zone, the mixing rate is not affected by the junction angles, which has an exponential relation with the downstream distance.